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vigra/sifImport.hxx
00001 /************************************************************************/
00002 /*                                                                      */
00003 /*       Copyright 2010 by Joachim Schleicher and Ullrich Koethe        */
00004 /*                                                                      */
00005 /*    This file is part of the VIGRA computer vision library.           */
00006 /*    The VIGRA Website is                                              */
00007 /*        http://hci.iwr.uni-heidelberg.de/vigra/                       */
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00009 /*        ullrich.koethe@iwr.uni-heidelberg.de    or                    */
00010 /*        vigra@informatik.uni-hamburg.de                               */
00011 /*                                                                      */
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00019 /*    conditions:                                                       */
00020 /*                                                                      */
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00023 /*    Software.                                                         */
00024 /*                                                                      */
00025 /*    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND    */
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00027 /*    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND          */
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00032 /*    OTHER DEALINGS IN THE SOFTWARE.                                   */
00033 /*                                                                      */
00034 /************************************************************************/
00035 
00036 
00037 /*                                                          
00038  *  Opens an Andor .sif file as MultiImageView.             
00039  *  The width, height and number of images are extracted    
00040  *  from the ASCII encoded variable length header.          
00041  *                                                          
00042  *  Based on the Java-Code from                             
00043  *  http://rsb.info.nih.gov/ij/plugins/open-sif.html        
00044  *  written by                                              
00045  *  L. Stirling Churchman (stirling at stanford.edu)        
00046  *  Philippe Carl (pcarl at uni-muenster.de)                
00047  *  Yoshiyuki Arai (arai at phys1.med.osaka-u.ac.jp)        
00048  *                                                          
00049  *  Currently tested SIF versions: 4.16.12005.0             
00050  *                                 4.16.30001.0             
00051  *                                 4. 6.    3.0             
00052 */
00053 
00054 #ifndef VIGRA_SIFIMPORT_HXX
00055 #define VIGRA_SIFIMPORT_HXX
00056 
00057 #include <fstream>
00058 #include <cstring>
00059 #include <cstddef>
00060 #include <vector> 
00061 #include "vigra/multi_array.hxx"
00062 
00063 namespace vigra {
00064  
00065  
00066  /** \addtogroup VigraSIFImport Import of Images from Andor Cameras
00067 
00068     Read an Andor SIF file into a MultiArrayView.
00069 **/
00070 //@{
00071 
00072 /********************************************************/
00073 /*                                                      */
00074 /*                   SIFImportInfo                      */
00075 /*                                                      */
00076 /********************************************************/
00077 /** \brief Extracts image properties from an Andor SIF file header.
00078 
00079 See \ref readSIF() for a usage example. This object must be
00080 used to read the image header of an Andor SIF file
00081 and enquire its properties.
00082 
00083 <b>\#include</b> <<a href="sifImport_8hxx_source.html">vigra/hdf5impex.hxx</a>><br>
00084 Namespace: vigra
00085 **/
00086 class SIFImportInfo
00087 {
00088     public:
00089         /** Construct SIFImportInfo object.
00090 
00091             The header of the Andor SIF file \a filename is accessed to 
00092             read the image properties. 
00093             
00094             \code
00095             SIFImportInfo info(filename);
00096             \endcode
00097          **/
00098         VIGRA_EXPORT SIFImportInfo(const char* filename);
00099 
00100         /** Get the width in pixels.
00101          **/
00102         VIGRA_EXPORT const int width() const;
00103 
00104         /** Get the height in pixels.
00105          **/
00106         VIGRA_EXPORT const int height() const;
00107 
00108         /** Get the stacksize, that is the number of 
00109          *  images contained in the dataset.
00110          **/
00111         VIGRA_EXPORT const int stacksize() const;
00112 
00113         /** Get the offset to the beginning of the actual data.
00114          *  Everything before this point belongs to the 
00115          *  variable lenght header.
00116          **/
00117         VIGRA_EXPORT const ptrdiff_t getOffset() const;
00118 
00119         /** Get the filename of this SIF object.
00120          **/
00121         VIGRA_EXPORT const char * getFileName() const;
00122 
00123         /** Output all information such as shutter, Temperature etc. 
00124            as human readable output.
00125           
00126         <b> Usage:</b>
00127         
00128         <b>\#include</b> <<a href="sifImport_8hxx_source.html">vigra/sifImport.hxx</a>><br>
00129         Namespace: vigra
00130         
00131         \code
00132         SIFImportInfo info(filename);
00133         std::cout << info << std::endl; // print infos to the console
00134 
00135         \endcode
00136          **/
00137         VIGRA_EXPORT friend std::ostream& operator<<(std::ostream& os, const SIFImportInfo& info);
00138 
00139     private:
00140         const char* m_filename;
00141         int m_width;
00142         int m_height;
00143         int m_stacksize;
00144         ptrdiff_t m_offset;
00145         int mod;
00146         int left, right, bottom, top;
00147         int xbin, ybin, xres, yres;
00148         int headerlen;
00149         double readout;
00150         double temperature1, temperature2;
00151         long long d;
00152         std::string cycleTime, temperature, exposureTime, EMGain,
00153         verticalShiftSpeed, version, model, originalFilename, preAmpGain;   
00154         size_t filesize;
00155     
00156 };
00157 
00158 
00159 
00160 
00161     /** \brief Read the image data specified by the given \ref vigra::SIFImportInfo object
00162                 and write them into the given 'array'.
00163                 
00164     The array must have the correct number of dimensions and shape for the dataset 
00165     represented by 'info'. 
00166     
00167     <b> Declaration:</b>
00168     
00169     \code
00170     namespace vigra {
00171         void 
00172         readSIF(const SIFImportInfo &info, MultiArrayView<3, float, UnstridedArrayTag> array);
00173     }
00174     \endcode
00175     
00176     <b> Usage:</b>
00177     
00178     <b>\#include</b> <<a href="sifImport_8hxx_source.html">vigra/sifImport.hxx</a>><br>
00179     Namespace: vigra
00180     
00181     \code
00182     SIFImportInfo info(filename);
00183 
00184     // create a 3D array of appropriate size
00185     typedef MultiArray<3, float>::difference_type Shape;
00186     MultiArray<3, float> in(Shape(info.width(), info.height(), info.stacksize()));
00187 
00188     readSIF(info, in); 
00189     \endcode
00190 */
00191 VIGRA_EXPORT void readSIF(const SIFImportInfo &info, MultiArrayView<3, float, UnstridedArrayTag> array);
00192 
00193 VIGRA_EXPORT std::ostream& operator<<(std::ostream& os, const SIFImportInfo& info);
00194 
00195 //@}
00196 
00197 } // namespace vigra
00198 
00199 #endif // VIGRA_SIFIMPORT_HXX

© Ullrich Köthe (ullrich.koethe@iwr.uni-heidelberg.de)
Heidelberg Collaboratory for Image Processing, University of Heidelberg, Germany

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